There is no spare independent bus that is set up by default.
I2C as a protocol supports multiple hosts and multiple devices, and the Linux kernel manages transactions when multiple processes are using the same bus concurrently, so it should be possible to just use the Navigator’s exposed I2C6 ports. The main potential caveat there is that the ArduPilot firmware may try to probe your device, especially if its address matches one of a valid sensor from ArduPilot’s libraries. That probing is most likely a one-time event, but that may vary depending on the driver.
Note that if it’s necessary it’s possible to create an extra software-defined I2C bus with GPIO pins, but doing the relevant pin reconfiguring may be a bit messy. If you need to go down that approach, it would likely make the most sense to do with pins on one of the Navigator’s SERIAL ports, and then disable that port in your autopilot parameters.
Can you provide more details or point me to documentation for this? “pins on one of the Navigator’s SERIAL ports, and then disable that port in your autopilot parameters” How do I disable a serial port using the autopilot parameters?